I do not see that behavior, as shown in the example below. Can you post an example?
By the way, aggregate is not part of the dplyr package, it is in the stats package.
set.seed(123)
DF <- data.frame(Name=sample(LETTERS[1:2],10,replace = TRUE),
Place=sample(LETTERS[3:4],10,replace = TRUE),
Value=rnorm(10))
aggregate(Value~Name+Place,data = DF,FUN = mean)
#> Name Place Value
#> 1 A C 0.1142822
#> 2 B C -0.0230071
#> 3 A D 0.3572065
#> 4 B D 0.4978505
aggregate(DF$Value,by=list(DF$Name,DF$Place),FUN=mean)
#> Group.1 Group.2 x
#> 1 A C 0.1142822
#> 2 B C -0.0230071
#> 3 A D 0.3572065
#> 4 B D 0.4978505